We propose to use high resolution proton two dimensional NMR structural and hydrogen exchange techniques to monitor complex formation between a series of antitumor agents and their sequence specific binding sites on deoxyoligonucleotides of defined sequence. The antitumor agents form a diverse class and include the bis-intercalating quinoxalines echinomycin and triostin which bind at dC-dG sites and TANDEM which binds at dT-dA sites. The experiments will probe for Hoogsteen base pair formation adjacent to the binding site and monitor the propagation of such perturbations along the helix. The aureolyic antitiumor agents chromomycin and mithramycin recognized and complex to dG-dG sites and we shall attempt to distinguish between potential intercalative and groove bindign modes, as well as establish intermolecular interactions involving the five attached hexapyranoses. The athracycline antitumor agents nogalamycin and bis(diethylamino)ethylamino) substituted anthraquinones are known to intercalate into DNA at alternating pyrimidine-purine sequences. We shall attempt to establish the overlap geometries at the intercalation site, the orientation of the bulky side chains in the minor and major grooves and the intermolecular interactions that stabilize the complex. The above studies will be undertaken on oligonucleotides extending from tetranucleotide to decanucleotide duplexes and attempts will be made to quantitate the nuclear Overhauser effect based distance constrains to define intermolecular interactions in the complex. These NMR experiments will be extended to binding studies of synthetic oligo(N-methylpyrrolecarboxaminde)s and their chiral analogs to A.T rich regions in oligonucleotide duplexes to check the principle of bifurcated hydrogen bonding, as well as rules governing chiral recognition in intermolecular interactions. Studies will also be undertaken on lexitropsins where the pyrrole specificity for A.T base pairs is replaced by imidazole specificity for G.C base pairs. Finally, the separate and simultaneous binding of two antitumor agents on adjacent sites of oligonucleotide duplexes will be investigated to probe for synergistic binding associated with combination chemotherapy.

Agency
National Institute of Health (NIH)
Institute
National Cancer Institute (NCI)
Type
Research Project (R01)
Project #
5R01CA046778-02
Application #
3190158
Study Section
Bio-Organic and Natural Products Chemistry Study Section (BNP)
Project Start
1988-04-01
Project End
1993-03-31
Budget Start
1989-04-01
Budget End
1990-03-31
Support Year
2
Fiscal Year
1989
Total Cost
Indirect Cost
Name
Columbia University (N.Y.)
Department
Type
Schools of Medicine
DUNS #
064931884
City
New York
State
NY
Country
United States
Zip Code
10027
Pitt, Stephen W; Zhang, Qi; Patel, Dinshaw J et al. (2005) Evidence that electrostatic interactions dictate the ligand-induced arrest of RNA global flexibility. Angew Chem Int Ed Engl 44:3412-5
Pitt, Stephen W; Majumdar, Ananya; Serganov, Alexander et al. (2004) Argininamide binding arrests global motions in HIV-1 TAR RNA: comparison with Mg2+-induced conformational stabilization. J Mol Biol 338:7-16
Mathy, Nathalie; Pellegrini, Olivier; Serganov, Alexander et al. (2004) Specific recognition of rpsO mRNA and 16S rRNA by Escherichia coli ribosomal protein S15 relies on both mimicry and site differentiation. Mol Microbiol 52:661-75
Ehresmann, Chantal; Ehresmann, Bernard; Ennifar, Eric et al. (2004) Molecular mimicry in translational regulation: the case of ribosomal protein S15. RNA Biol 1:66-73
Serganov, Alexander; Polonskaia, Ann; Ehresmann, Bernard et al. (2003) Ribosomal protein S15 represses its own translation via adaptation of an rRNA-like fold within its mRNA. EMBO J 22:1898-908
Al-Hashimi, Hashim M; Pitt, Stephen W; Majumdar, Ananya et al. (2003) Mg2+-induced variations in the conformation and dynamics of HIV-1 TAR RNA probed using NMR residual dipolar couplings. J Mol Biol 329:867-73
Stelzl, Ulrich; Zengel, Janice M; Tovbina, Marina et al. (2003) RNA-structural mimicry in Escherichia coli ribosomal protein L4-dependent regulation of the S10 operon. J Biol Chem 278:28237-45
Odell, Mark; Malinina, Lucy; Sriskanda, Verl et al. (2003) Analysis of the DNA joining repertoire of Chlorella virus DNA ligase and a new crystal structure of the ligase-adenylate intermediate. Nucleic Acids Res 31:5090-100
Al-Hashimi, Hashim M; Patel, Dinshaw J (2002) Residual dipolar couplings: synergy between NMR and structural genomics. J Biomol NMR 22:1-8
Ye, Keqiong; Serganov, Alexander; Hu, Weidong et al. (2002) Ribosome-associated factor Y adopts a fold resembling a double-stranded RNA binding domain scaffold. Eur J Biochem 269:5182-91

Showing the most recent 10 out of 31 publications